This is not a complete index of variables and faces, only the ones that are mentioned in the manual. For a more complete list, use M-x org-customize <RET> and then click yourself through the tree.
cdlatex-simplify-sub-super-scripts: CDLaTeX modeconstants-unit-system: In-buffer settingsconstants-unit-system: Referenceshtmlize-output-type: Exporting Agenda ViewsLaTeX-verbatim-environments: A LaTeX exampleorg-adapt-indentation: Clean vieworg-agenda-add-entry-text-maxlines: Exporting Agenda Viewsorg-agenda-columns-add-appointments-to-effort-sum: Effort estimatesorg-agenda-confirm-kill: Agenda commandsorg-agenda-custom-commands: Setting Optionsorg-agenda-custom-commands: Storing searchesorg-agenda-custom-commands: Extracting agenda informationorg-agenda-custom-commands: Setting Optionsorg-agenda-custom-commands: Sparse treesorg-agenda-diary-file: Agenda commandsorg-agenda-dim-blocked-tasks: TODO dependenciesorg-agenda-entry-text-maxlines: Agenda commandsorg-agenda-exporter-settings: Agenda commandsorg-agenda-exporter-settings: Exporting Agenda Viewsorg-agenda-files: iCalendar exportorg-agenda-files: Sorting of agenda itemsorg-agenda-files: Agenda filesorg-agenda-filter-preset: Agenda commandsorg-agenda-log-mode-items: Agenda commandsorg-agenda-ndays: Agenda commandsorg-agenda-ndays: Weekly/daily agendaorg-agenda-overriding-header: Special agenda viewsorg-agenda-prefix-format: Presentation and sortingorg-agenda-restore-windows-after-quit: Agenda Viewsorg-agenda-show-inherited-tags: Agenda commandsorg-agenda-skip-archived-trees: Internal archivingorg-agenda-skip-function: Using the mapping APIorg-agenda-skip-function: Special agenda viewsorg-agenda-skip-scheduled-if-done: Deadlines and schedulingorg-agenda-sorting-strategy: Sorting of agenda itemsorg-agenda-start-with-clockreport-mode: Agenda commandsorg-agenda-start-with-entry-text-mode: Agenda commandsorg-agenda-start-with-follow-mode: Agenda commandsorg-agenda-tags-todo-honor-ignore-options: Matching tags and propertiesorg-agenda-text-search-extra-files: Agenda dispatcherorg-agenda-text-search-extra-files: Search vieworg-agenda-time-grid: Time-of-day specificationsorg-agenda-time-grid: Agenda commandsorg-agenda-todo-ignore-deadlines: Global TODO listorg-agenda-todo-ignore-scheduled: Global TODO listorg-agenda-todo-ignore-with-date: Global TODO listorg-agenda-todo-list-sublevels: Global TODO listorg-agenda-todo-list-sublevels: Breaking down tasksorg-agenda-use-time-grid: Agenda commandsorg-agenda-use-time-grid: Time-of-day specificationsorg-agenda-window-setup: Agenda Viewsorg-archive-default-command: Agenda commandsorg-archive-default-command: Archivingorg-archive-location: In-buffer settingsorg-archive-location: Moving subtreesorg-archive-save-context-info: Moving subtreesorg-attach-directory: Attachmentsorg-attach-method: Attachmentsorg-babel-default-header-args: Header arguments in Org-mode propertiesorg-babel-default-header-args: System-wide header argumentsorg-calc-default-modes: Formula syntax for Calcorg-clock-idle-time: Resolving idle timeorg-clock-into-drawer: Clocking work timeorg-clock-modeline-total: Clocking work timeorg-coderef-label-format: Literal examplesorg-columns-default-format: Agenda column vieworg-columns-default-format: Using column vieworg-columns-default-format: Agenda commandsorg-columns-default-format: Effort estimatesorg-columns-skip-archived-trees: Internal archivingorg-combined-agenda-icalendar-file: iCalendar exportorg-confirm-babel-evaluate: Code evaluation securityorg-confirm-elisp-link-function: Code evaluation securityorg-confirm-shell-link-function: Code evaluation securityorg-create-file-search-functions: Custom searchesorg-ctrl-c-ctrl-c-hook: Context-sensitive commandsorg-ctrl-k-protect-subtree: Headlinesorg-cycle-emulate-tab: Visibility cyclingorg-cycle-global-at-bob: Visibility cyclingorg-cycle-include-plain-lists: Plain listsorg-cycle-open-archived-trees: Internal archivingorg-cycle-separator-lines: Headlinesorg-deadline-warning-days: Deadlines and schedulingorg-deadline-warning-days: Inserting deadline/scheduleorg-default-notes-file: Setting up captureorg-default-notes-file: Template elementsorg-default-priority: In-buffer settingsorg-default-priority: Prioritiesorg-display-custom-times: Custom time formatorg-display-custom-times: Publishing optionsorg-display-internal-link-with-indirect-buffer: Handling linksorg-disputed-keys: Conflictsorg-done (face): Faces for TODO keywordsorg-drawers: Drawersorg-drawers: In-buffer settingsorg-effort-property: Effort estimatesorg-empty-line-terminates-plain-lists: Plain listsorg-enable-table-editor: Built-in table editororg-enforce-todo-dependencies: TODO dependenciesorg-entities: Special charactersorg-entities: Special symbolsorg-execute-file-search-functions: Custom searchesorg-export-ascii-links-to-notes: ASCII/Latin-1/UTF-8 exportorg-export-author-info: Publishing optionsorg-export-creator-info: Publishing optionsorg-export-default-language: Publishing optionsorg-export-default-language: Export optionsorg-export-docbook-default-image-attributes: Images in DocBook exportorg-export-docbook-doctype: Special charactersorg-export-docbook-inline-image-extensions: Images in DocBook exportorg-export-docbook-xsl-fo-proc-command: DocBook export commandsorg-export-docbook-xslt-proc-command: DocBook export commandsorg-export-docbook-xslt-stylesheet: DocBook export commandsorg-export-email: Publishing optionsorg-export-exclude-tags: Publishing optionsorg-export-exclude-tags: Selective exportorg-export-headline-levels: Publishing optionsorg-export-headline-levels: Headings and sectionsorg-export-highlight-first-table-line: Publishing optionsorg-export-html-auto-postamble: Publishing optionsorg-export-html-auto-preamble: Publishing optionsorg-export-html-expand: Publishing optionsorg-export-html-extension: Publishing optionsorg-export-html-extra: CSS supportorg-export-html-inline-images: Publishing optionsorg-export-html-inline-images: Images in HTML exportorg-export-html-link-home: Publishing optionsorg-export-html-link-org-files-as-html: Publishing optionsorg-export-html-link-up: Publishing optionsorg-export-html-postamble: Publishing optionsorg-export-html-preamble: Publishing optionsorg-export-html-style: Publishing optionsorg-export-html-style: CSS supportorg-export-html-style-default: CSS supportorg-export-html-style-extra: Publishing optionsorg-export-html-style-include-default: Publishing optionsorg-export-html-style-include-default: CSS supportorg-export-html-table-tag: Publishing optionsorg-export-html-table-tag: Tables in HTML exportorg-export-html-tag-class-prefix: CSS supportorg-export-html-todo-kwd-class-prefix: CSS supportorg-export-html-use-infojs: JavaScript supportorg-export-html-with-timestamp: Publishing optionsorg-export-latex-classes: Header and sectioningorg-export-latex-default-class: Header and sectioningorg-export-latex-default-packages-alist: Header and sectioningorg-export-latex-packages-alist: Header and sectioningorg-export-preserve-breaks: Publishing optionsorg-export-publishing-directory: Publishing optionsorg-export-run-in-background: The export dispatcherorg-export-section-number-format: Publishing optionsorg-export-select-tags: Publishing optionsorg-export-select-tags: Selective exportorg-export-skip-text-before-1st-heading: Initial textorg-export-skip-text-before-1st-heading: Publishing optionsorg-export-taskjuggler-default-reports: TaskJuggler exportorg-export-taskjuggler-project-tag: TaskJuggler exportorg-export-taskjuggler-resource-tag: TaskJuggler exportorg-export-with-archived-trees: Publishing optionsorg-export-with-archived-trees: Internal archivingorg-export-with-drawers: Publishing optionsorg-export-with-emphasize: Publishing optionsorg-export-with-fixed-width: Publishing optionsorg-export-with-footnotes: Publishing optionsorg-export-with-LaTeX-fragments: Publishing optionsorg-export-with-priority: Publishing optionsorg-export-with-section-numbers: Publishing optionsorg-export-with-special-strings: Publishing optionsorg-export-with-sub-superscripts: Publishing optionsorg-export-with-sub-superscripts: Subscripts and superscriptsorg-export-with-tables: Publishing optionsorg-export-with-tags: Publishing optionsorg-export-with-TeX-macros: Publishing optionsorg-export-with-timestamps: Publishing optionsorg-export-with-toc: Publishing optionsorg-export-with-toc: Table of contentsorg-export-with-todo-keywords: Publishing optionsorg-fast-tag-selection-include-todo: Fast access to TODO statesorg-fast-tag-selection-single-key: Setting tagsorg-file-apps: Handling linksorg-file-apps: Attachmentsorg-footnote-auto-adjust: In-buffer settingsorg-footnote-auto-adjust: Footnotesorg-footnote-auto-label: In-buffer settingsorg-footnote-auto-label: Footnotesorg-footnote-define-inline: In-buffer settingsorg-footnote-define-inline: Footnotesorg-footnote-section: Footnotesorg-format-latex-header: LaTeX fragmentsorg-format-latex-options: LaTeX fragmentsorg-format-latex-options: Previewing LaTeX fragmentsorg-from-is-user-regexp: Template expansionorg-global-properties: Property syntaxorg-global-properties: Effort estimatesorg-goto-auto-isearch: Motionorg-goto-interface: Motionorg-hide (face): Clean vieworg-hide-block-startup: Blocksorg-hide-leading-stars: In-buffer settingsorg-hide-leading-stars: Clean vieworg-hierarchical-checkbox-statistics: Checkboxesorg-hierarchical-todo-statistics: Breaking down tasksorg-highest-priority: In-buffer settingsorg-highest-priority: Prioritiesorg-icalendar-categories: iCalendar exportorg-icalendar-include-body: iCalendar exportorg-icalendar-include-todo: iCalendar exportorg-icalendar-store-UID: iCalendar exportorg-icalendar-use-deadline: iCalendar exportorg-icalendar-use-scheduled: iCalendar exportorg-imenu-depth: Cooperationorg-infojs-options: JavaScript supportorg-insert-mode-line-in-empty-file: Activationorg-irc-link-to-logs: Handling linksorg-keep-stored-link-after-insertion: Handling linksorg-latex-low-levels: LaTeX/PDF export commandsorg-link-abbrev-alist: In-buffer settingsorg-link-abbrev-alist: Link abbreviationsorg-link-to-org-use-id: Handling linksorg-list-demote-modify-bullet: Plain listsorg-log-done: Agenda commandsorg-log-done: In-buffer settingsorg-log-done: Tracking TODO state changesorg-log-into-drawer: Tracking TODO state changesorg-log-into-drawer: Agenda commandsorg-log-note-clock-out: In-buffer settingsorg-log-note-clock-out: Clocking work timeorg-log-refile: Refiling notesorg-log-repeat: Repeated tasksorg-log-repeat: In-buffer settingsorg-log-states-order-reversed: Tracking TODO state changesorg-lowest-priority: Prioritiesorg-lowest-priority: In-buffer settingsorg-M-RET-may-split-line: Plain listsorg-M-RET-may-split-line: Structure editingorg-odd-levels-only: In-buffer settingsorg-odd-levels-only: Clean vieworg-odd-levels-only: Matching tags and propertiesorg-odd-levels-only: Special agenda viewsorg-outline-path-complete-in-steps: Refiling notesorg-overriding-columns-format: Agenda column vieworg-popup-calendar-for-date-prompt: The date/time promptorg-priority-faces: Prioritiesorg-priority-start-cycle-with-default: Prioritiesorg-property-allowed-value-functions: Using the property APIorg-publish-project-alist: Project alistorg-publish-project-alist: Publishing optionsorg-publish-use-timestamps-flag: Triggering publicationorg-put-time-stamp-overlays: In-buffer settingsorg-read-date-display-live: The date/time promptorg-read-date-prefer-future: The date/time promptorg-refile-allow-creating-parent-nodes: Refiling notesorg-refile-targets: Refiling notesorg-refile-use-cache: Refiling notesorg-refile-use-outline-path: Refiling notesorg-remove-highlights-with-change: Clocking work timeorg-remove-highlights-with-change: Sparse treesorg-replace-disputed-keys: Conflictsorg-reverse-note-order: Refiling notesorg-show-entry-below: Sparse treesorg-show-following-heading: Sparse treesorg-show-hierarchy-above: Sparse treesorg-show-siblings: Sparse treesorg-sort-agenda-noeffort-is-high: Agenda commandsorg-sparse-tree-open-archived-trees: Internal archivingorg-special-ctrl-a/e: Headlinesorg-special-ctrl-k: Headlinesorg-speed-commands-user: Speed keysorg-startup-align-all-tables: In-buffer settingsorg-startup-align-all-tables: Column width and alignmentorg-startup-folded: Visibility cyclingorg-startup-folded: In-buffer settingsorg-startup-indented: In-buffer settingsorg-store-link-functions: Adding hyperlink typesorg-stuck-projects: Stuck projectsorg-support-shift-select: Plain listsorg-support-shift-select: Conflictsorg-table-auto-blank-field: Built-in table editororg-table-copy-increment: Built-in table editororg-table-export-default-format: Built-in table editororg-table-formula: In-buffer settingsorg-table-formula-constants: Cooperationorg-table-formula-constants: In-buffer settingsorg-table-formula-constants: Referencesorg-table-use-standard-references: Editing and debugging formulasorg-tag-alist: Setting tagsorg-tag-alist: In-buffer settingsorg-tag-faces: Tagsorg-tag-persistent-alist: Setting tagsorg-tags-column: Setting tagsorg-tags-exclude-from-inheritance: Tag inheritanceorg-tags-match-list-sublevels: Matching tags and propertiesorg-tags-match-list-sublevels: Tag searchesorg-tags-match-list-sublevels: Tag inheritanceorg-tags-match-list-sublevels: Property searchesorg-time-stamp-custom-formats: Custom time formatorg-time-stamp-overlay-formats: In-buffer settingsorg-time-stamp-rounding-minutes: Creating timestampsorg-todo (face): Faces for TODO keywordsorg-todo-keyword-faces: Faces for TODO keywordsorg-todo-keywords: TODO extensionsorg-todo-keywords: In-buffer settingsorg-todo-keywords: TODO basicsorg-todo-keywords: Global TODO listorg-todo-repeat-to-state: Repeated tasksorg-todo-state-tags-triggers: TODO basicsorg-track-ordered-property-with-tag: Checkboxesorg-track-ordered-property-with-tag: TODO dependenciesorg-treat-insert-todo-heading-as-state-change: Structure editingorg-treat-S-cursor-todo-selection-as-state-change: TODO basicsorg-use-property-inheritance: iCalendar exportorg-use-property-inheritance: Using the property APIorg-use-property-inheritance: Property inheritanceorg-use-speed-commands: Speed keysorg-use-tag-inheritance: Tag inheritanceorg-yank-adjusted-subtrees: Structure editingorg-yank-folded-subtrees: Structure editingparse-time-months: The date/time promptparse-time-weekdays: The date/time promptps-landscape-mode: Exporting Agenda Viewsps-number-of-columns: Exporting Agenda Viewsuser-full-name: Export optionsuser-full-name: Publishing optionsuser-mail-address: Publishing optionsuser-mail-address: Export options